S. Sahoo

Dynamical properties of chromatin provide insights into key folding principles

The paper shows that loop extrusion dominates dynamic properties of chromatin, even when intra-chromatin interactions dominate static structure.

A novel human model to deconvolve cell-intrinsic phenotypes of genetically dysregulated pathways in lung squamous cell carcinoma

The paper develops an in vitro model of lung squamous cell carcinoma using primary human bronchial epithelial cells to study genotype-phenotype relationships in cancer progression.

Anoikis resistance and metastasis of ovarian cancer can be overcome by CDK8/19 Mediator kinase inhibition.

This study shows CDK8/19 inhibition can reverse anoikis resistance and metastasis in ovarian cancer by altering transcriptional programs.

Outer membrane proteins in Mycobacterium tuberculosis and its potential role in small molecule permeation

This study identifies outer membrane proteins in Mycobacterium tuberculosis involved in small molecule permeation, with potential applications for improving anti-TB drug efficacy.

Mutually exclusive teams-like patterns of gene regulation characterize phenotypic heterogeneity along the noradrenergic-mesenchymal axis in neuroblastoma

The paper identifies mutually exclusive gene regulation patterns between noradrenergic and mesenchymal states in neuroblastoma, linking them to phenotypic plasticity and therapy resistance.

Nonequilibrium switching of segmental states can influence compaction of chromatin

This paper presents a diblock copolymer model of chromatin that simulates nonequilibrium switching between segmental states, showing how this affects chromatin compaction and contact probabilities.

GPX4-VIM equates a proliferating DTP state in TNBC subtypes with converged vulnerabilities to autophagy and glutathione inhibition.

The paper identifies a proliferating DTP state in TNBC subtypes that is vulnerable to autophagy and glutathione inhibition, linking GPX4-VIM expression to survival outcomes.

Melanocytes Exhibit Distinct Cell States Governed by A Gene Regulatory Network Under Stochastic Influence

The paper identifies distinct melanocyte states and shows stochastic gene expression and epigenetic modification enable their co-existence and response to environmental cues.

Dynamical modelling of proliferative-invasive plasticity and IFN-gamma signaling in melanoma reveals mechanisms of PD-L1 expression heterogeneity

This study uses dynamical modeling to uncover how IFN-gamma signaling and proliferative-invasive transitions shape PD-L1 expression heterogeneity in melanoma, with experimental validation in cell lines and datasets.

Acquisition of hybrid E/M phenotype associated with increased migration, drug resistance and stemness is mediated by reduced miR-18a levels in ER-negative breast cancer

This study shows that low miR-18a levels in ER-negative breast cancer drive hybrid E/M cell traits linked to migration, drug resistance, and stemness.

Cinemeducation improves early clinical exposure to Inborn Errors of Metabolism

This study evaluates the use of cinemeducation to improve student interest, satisfaction, and academic performance in learning about Inborn Errors of Metabolism.

The ELF3 transcription factor is associated with an epithelial phenotype and represses epithelial-mesenchymal transition

The paper identifies ELF3 as an epithelial-associated transcription factor that inhibits EMT and stabilizes hybrid E/M phenotypes, with potential prognostic implications in solid tumors.

A comprehensive single cell data analysis of in lymphoblastoid cells reveals the role of Super-enhancers in maintaining EBV latency

This study uses scRNA-seq to analyze EBV latency in lymphoblastoid cells, identifying two distinct clusters with different EBV gene expression and revealing the role of super-enhancers in maintaining latency.

P4HA2: A link between tumor-intrinsic hypoxia, partial EMT and collective migration

This study identifies P4HA2 as a central regulator linking tumor-intrinsic hypoxia, partial EMT, and collective migration using microtumor models and differential gene expression analysis.

Quantifying the patterns of metabolic plasticity and heterogeneity along the epithelial-hybrid-mesenchymal spectrum in cancer

The paper analyzes metabolic pathway associations with EMT status across cancer datasets, revealing both general trends and heterogeneity in metabolic plasticity.

Identification of mRNAs that undergo stop codon readthrough in Arabidopsis thaliana

This study identifies 144 Arabidopsis thaliana genes undergoing stop codon readthrough using ribosome profiling and experimental validation, revealing functional implications for protein localization and plant physiology.

KLF4 induces Mesenchymal-Epithelial Transition (MET) by suppressing multiple EMT-inducing transcription factors

This study shows KLF4 suppresses EMT-inducing transcription factors and promotes MET, acting as a potential MET-TF with implications for cancer survival.

Dual avatars of E. coli grxB encoded Glutaredoxin 2 perform ascorbate recycling and ion channel activities

This study identifies two functional roles of EcGrx2: ascorbate recycling and ion channel activity, revealing its role in antioxidant defense and membrane integration in E. coli.

Immunosuppressive traits of the hybrid epithelial/mesenchymal phenotype

The paper investigates immune-evasive strategies of hybrid epithelial/mesenchymal (E/M) cells using a regulatory network model and RNA-seq data, showing they can exhibit high PD-L1 levels without full EMT.

Zinc2+ ion inhibits SARS-CoV-2 main protease and viral replication in vitro.

This study shows that zinc ions inhibit SARS-CoV-2 main protease and viral replication in vitro, with structural evidence supporting the mechanism.

A mechanistic model captures the emergence and implications of non-genetic heterogeneity and reversible drug resistance in ER+ breast cancer cells

This study develops a mechanistic model showing how non-genetic heterogeneity and reversible drug resistance in ER+ breast cancer cells arise through EMT dynamics and phenotypic plasticity, suggesting MET inducers as potential therapeutic targets.

MITOCHONDRIAL GENOME REVEALS CONTRASTING PATTERN OF ADAPTIVE SELECTION IN TURTLES AND TORTOISES

The paper analyzes mitochondrial genomes of turtles and tortoises to compare adaptive selection patterns, finding stronger positive selection in turtles than tortoises.

Hybrid E/M phenotype(s) and stemness: a mechanistic connection embedded in network topology

This study develops a mathematical model to show hybrid epithelial/mesenchymal (E/M) phenotypes are more likely to acquire stemness than pure epithelial or mesenchymal states.

A computational systems biology approach identifies SLUG as a mediator of partial Epithelial-Mesenchymal Transition (EMT)

This study identifies SLUG as a stabilizer of hybrid epithelial/mesenchymal phenotypes through computational systems biology analysis.

Nanotrap(R) particles improve detection of SARS-CoV-2 for pooled sample methods, extraction-free saliva methods, and extraction-free medium methods

This paper introduces a method using Nanotrap(R) particles to improve SARS-CoV-2 detection in pooled samples, saliva, and transport medium by concentrating virus before RNA extraction.

Exosome-mediated MIR211 modulates tumor microenvironment via the DUSP6-ERK5 axis and contributes to BRAFV600E inhibitor resistance in melanoma.

This study shows MIR211 promotes melanoma growth and resistance to BRAF inhibitors by modulating the DUSP6-ERK5 axis via exosome transfer in the tumor microenvironment.